Bottom Line:
An miRNA seed sequence analysis suggested that these miRNAs regulate several critical immune-related genes including SLC11A1, PIGE-108A11.3 and VAV2.Furthermore, the expression of the proposed targets of miR-214 (SLC11A1 and PIGE-108A11.3) increased while that of the proposed target of miR-331-3p (VAV2) decreased following challenge (expression changes confirmed by in vitro assays).Based on these observations, we propose potential roles for miR-214 and miR-331-3p in regulation of immune responses to Salmonella infection.

ABSTRACTTo understand the role of miRNAs in regulating genes involved in host response to bacterial infection and shedding of foodborne pathogens, a systematic profiling of miRNAs and mRNAs from the whole blood of pigs upon Salmonella challenge was performed. A total of 62 miRNAs were differentially expressed post infection (false discovery rate <0.1). An integrative analysis of both the differentially expressed miRNAs and mRNAs using sequence-based miRNA target prediction and negative correlation of miRNA-mRNA profiles helped identify miRNA-mRNA networks that may potentially regulate host response to Salmonella infection. From these networks, miR-214 and miR-331-3p were identified as new candidates potentially associated with Salmonella infection. An miRNA seed sequence analysis suggested that these miRNAs regulate several critical immune-related genes including SLC11A1, PIGE-108A11.3 and VAV2. We showed that challenged pigs had reduced miR-214 expression and increased miR-331-3p expression in the whole blood. Furthermore, the expression of the proposed targets of miR-214 (SLC11A1 and PIGE-108A11.3) increased while that of the proposed target of miR-331-3p (VAV2) decreased following challenge (expression changes confirmed by in vitro assays). Based on these observations, we propose potential roles for miR-214 and miR-331-3p in regulation of immune responses to Salmonella infection.

f2: Differentially expressed (DE) mRNAs in response to Salmonella infection.MA plot (a) and volcano plot (b) showing DE mRNAs after Salmonella infection. The names of top three most significant DE genes are shown.

Mentions:
We analyzed the correlation between blood cell type count (lymphocyte, monocyte, neutrophil, eosinophil, and basophil counts) and the expression levels of mRNAs, and observed that the expression levels of 75 mRNAs were positively correlated (BH corrected p < 0.01) with one or more blood cell type counts and these mRNAs were excluded from further analyses. The mRNA data also revealed dramatic mRNA expression changes after challenge but few DE mRNAs between LS and PS samples. When analyzing LS and PS samples together, a total of 4443 DE genes were identified between 0 dpi and 2 dpi (Table 1, Fig. 2). Compared to the PS samples (4136 DE genes), the changes in mRNA expression of LS samples (1584 DE genes) were less dramatic, which is also consistent with the results from the miRNA analysis (Table 1) and with a previous microarray-based study21. However, the degree of mRNA expression change is considerably higher compared to that of miRNA. The top 10 most significant DE mRNAs show an average logFC of 4.3, whereas the top 10 miRNAs only have logFC of 1.16. Several immune-related genes were found significantly DE after challenge. For example, the expression of IL22RA2 and NOD1 was significantly up-regulated following Salmonella challenge (logFC 6.38 and 3.60, respectively). Complete lists of differentially expressed mRNAs are provided in Supplementary Table S4.

f2: Differentially expressed (DE) mRNAs in response to Salmonella infection.MA plot (a) and volcano plot (b) showing DE mRNAs after Salmonella infection. The names of top three most significant DE genes are shown.

Mentions:
We analyzed the correlation between blood cell type count (lymphocyte, monocyte, neutrophil, eosinophil, and basophil counts) and the expression levels of mRNAs, and observed that the expression levels of 75 mRNAs were positively correlated (BH corrected p < 0.01) with one or more blood cell type counts and these mRNAs were excluded from further analyses. The mRNA data also revealed dramatic mRNA expression changes after challenge but few DE mRNAs between LS and PS samples. When analyzing LS and PS samples together, a total of 4443 DE genes were identified between 0 dpi and 2 dpi (Table 1, Fig. 2). Compared to the PS samples (4136 DE genes), the changes in mRNA expression of LS samples (1584 DE genes) were less dramatic, which is also consistent with the results from the miRNA analysis (Table 1) and with a previous microarray-based study21. However, the degree of mRNA expression change is considerably higher compared to that of miRNA. The top 10 most significant DE mRNAs show an average logFC of 4.3, whereas the top 10 miRNAs only have logFC of 1.16. Several immune-related genes were found significantly DE after challenge. For example, the expression of IL22RA2 and NOD1 was significantly up-regulated following Salmonella challenge (logFC 6.38 and 3.60, respectively). Complete lists of differentially expressed mRNAs are provided in Supplementary Table S4.

Bottom Line:
An miRNA seed sequence analysis suggested that these miRNAs regulate several critical immune-related genes including SLC11A1, PIGE-108A11.3 and VAV2.Furthermore, the expression of the proposed targets of miR-214 (SLC11A1 and PIGE-108A11.3) increased while that of the proposed target of miR-331-3p (VAV2) decreased following challenge (expression changes confirmed by in vitro assays).Based on these observations, we propose potential roles for miR-214 and miR-331-3p in regulation of immune responses to Salmonella infection.

ABSTRACTTo understand the role of miRNAs in regulating genes involved in host response to bacterial infection and shedding of foodborne pathogens, a systematic profiling of miRNAs and mRNAs from the whole blood of pigs upon Salmonella challenge was performed. A total of 62 miRNAs were differentially expressed post infection (false discovery rate <0.1). An integrative analysis of both the differentially expressed miRNAs and mRNAs using sequence-based miRNA target prediction and negative correlation of miRNA-mRNA profiles helped identify miRNA-mRNA networks that may potentially regulate host response to Salmonella infection. From these networks, miR-214 and miR-331-3p were identified as new candidates potentially associated with Salmonella infection. An miRNA seed sequence analysis suggested that these miRNAs regulate several critical immune-related genes including SLC11A1, PIGE-108A11.3 and VAV2. We showed that challenged pigs had reduced miR-214 expression and increased miR-331-3p expression in the whole blood. Furthermore, the expression of the proposed targets of miR-214 (SLC11A1 and PIGE-108A11.3) increased while that of the proposed target of miR-331-3p (VAV2) decreased following challenge (expression changes confirmed by in vitro assays). Based on these observations, we propose potential roles for miR-214 and miR-331-3p in regulation of immune responses to Salmonella infection.